I'd recommend that you should certainly drain and replace all the brake fluid. You should do it every 2 years anyway, so it makes no sense not to do it now. Do the clutch whilst you're at it.
Use DOT 4 fluid. Don't use a silicone based one (DOT 5).
Bleed the brakes as normal, starting with the nipple furthest from the master cylinder. I have used a Gunson easy bleed to great effect as I end up doing this on my own. They're cheap and provided you follow the instructions I get perfect results every time. (If you do use this, ensure that the tyre you're connecting to has no more than 10 PSI or you'll end up with brake fluid everywhere). If you're going to do the pedal method make sure you have a block under the clutch pedal to avoid over-extending the piston in the master cylinder.
Out of interest, how did you do the alignment of the rear axle when you put it back on? Did you follow the various methods on the site, (pipework frame, or the plumb bob).
JH